Cactus 2.3.0 2022-11-21

Update 2022-12-07: cactus-bin-v2.3.0.tar.gz fixed to include working vg binary. Thanks @leleory for noticing.

Cactus 2.3.0 is available in the following forms:

• Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.3.0
  GPU-accelerated Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.3.0-gpu
  Install instructions in README.md
• Pre-compiled Binaries Linux Tarball: cactus-bin-v2.3.0.tar.gz
  Install instructions in BIN-INSTALL.md
• Pre-compiled Binaries For Older CPU Architectures (no pangenome support) Linux Tarball: cactus-bin-legacy-v2.3.0.tar.gz
  Install instructions in BIN-INSTALL.md
• Source Tarball: cactus-v2.3.0.tar.gz
  Install instructions in README.md

WARNING: do not use the github automatically generated source files (Source code (zip) or Source code (tar.gz)), these are not correct.

The Docker images and binaries linked above are built using AVX2 extensions, and require a CPU that supports them, except the "Pre-compiled Binaries For Older CPU Architectures" which should be compatible with any 64-bit architecture (but don't yet support the Cactus's pangenome pipeline).

Please subscribe to the cactus-announce low-volume mailing list to receive notice of Cactus release.

Release Notes

This release contains substantial changes to the Minigraph-Cactus pangenome pipeline, namely in cactus-graphmap-join.

• The SAMPLE.HAPLOTYPE naming convention now only needed for non-haploid samples: you no longer need to add .0 to non-reference samples
• All paths, including reference, are stored as W-lines in the GFA output (previously the reference was stored as a P-line)
• XG/GBWT/GG output replaced with GBZ
• Latest vg now shipped with Cactus (was stuck at v.1.40.0 for a while). In most cases vg version >= 1.44.0 is now required to use the output.
• Giraffe indexing should now be more efficient
• cactus-graphmap-join now only needs to be run once. Previously, up to 3 times was suggested. The single invocation of cactus-graphmap-join can still create up to three graphs and sets of indexes. Sensible defaults are provided to encourage users to, for example, index the filtered graph.
• Many options from cactus-graphmap-join have been removed or moved into the config xml
• --delFilter now enabled by default in cactus-graphmap. In addition, it is broadened to disallow any contig from inducing a deletion greater than (half) its length. (this ratio can be controlled using the delFilterQuerySizeThreshold config parameter).
• cactus-graphmap-join will no longer ever produce a graphs with edges that aren't covered by any paths (was rare but possible before).
• minigraph version included update to fix assertion failure bug.
• mafTools binaries now included in Cactus.
• Toil caching turned off by default when using the slurm batch system.